The new boss of the APVMA says he will overhaul the agency as it relocates from Canberra.

Dr Chris Parker has officially become chief executive of the Australian Pesticides and Veterinary Medicines Authority (APVMA), taking over amid a controversial relocation of the pesticides regulator from Canberra to Armidale in NSW.

Dr Parker said the forced move “clearly presents a whole range of challenges” but insists it will be used as an opportunity to “reset the organisation”, focusing on performance and financial reforms.

Dr Parker said the APVMA's financial situation is “completely unsustainable”.

“We will not be able to sustain operational loses and we'll be in discussion with industry … about doing a full [cost recovery implementation strategy] associated with an increase or a change in our fee structure,” he said.

The APVMA has been operating at a loss for the past three years.

The relocation has already prompted several staff departures, including chief executive Kareena Arthy, who has since joined the ACT Government.

“We will see more staff making the decision to take jobs elsewhere and that's a perfectly legitimate choice for those staff to make,” Dr Parker said.

“Staff leaving is always a challenge in any organisation but I think we're well placed with a whole range of policies around incentive bonuses for staff to stay.”